Tools

"... In some applications of graph visualization, input edges have associated target lengths. Dealing with these lengths is a challenge, especially for large graphs. Stress models are often employed in this situation. However, the traditional full stress model is not scalable due to its reliance on an in ..."

In some applications of graph visualization, input edges have associated target lengths. Dealing with these lengths is a challenge, especially for large graphs. Stress models are often employed in this situation. However, the traditional full stress model is not scalable due to its reliance on an initial all-pairs shortest path calculation. A number of fast approximation algorithms have been proposed. While they work well for some graphs, the results are less satisfactory on graphs of intrinsically high dimension, because nodes overlap unnecessarily. We propose a solution, called the maxent-stress model, which applies the principle of maximum entropy to cope with the extra degrees of freedom. We describe a force-augmented stress majorization algorithm that solves the maxent-stress model. Numerical results show that the algorithm scales well, and provides acceptable layouts for large, non-rigid graphs. This also has potential applications to scalable algorithms for statistical multidimensional scaling (MDS) with variable distances.

...volved in stress majorization. Their approach works efficiently for the special case of wi j = 1/di j in (1). Although it essentially ignores edge lengths, the binary stress model of Koren and Civril =-=[27]-=- is stylistically related to ours, in that the first term attempts to specify edge lengths (as uniformly 0), the second term has the effect of uniformly spacing the nodes. Specifically, in that model,...

"... We describe an algorithm for radial layout of undirected graphs, in which nodes are constrained to concentric circles centered at the origin. Such constraints are typical, e.g., in the layout of social networks, when structural centrality is mapped to geometric centrality or when the primary intenti ..."

We describe an algorithm for radial layout of undirected graphs, in which nodes are constrained to concentric circles centered at the origin. Such constraints are typical, e.g., in the layout of social networks, when structural centrality is mapped to geometric centrality or when the primary intention of the layout is the display of the vicinity of a distinguished node. Our approach is based on an extension of stress minimization with a weighting scheme that gradually imposes radial constraints on the intermediate layout during the majorization process, and thus is an attempt to preserve as much information about the graph structure as possible. 1

... recently, other extensions of the stress term have been used for drawing graphs with explicitly formulated aesthetic criteria, such as the uniform scattering of the nodes in a graph over a unit disk =-=[20]-=-, penalizing node overlaps [15], or preserving a given topology [13]. 1All these approaches modify the target distances themselves in one form or another, while the approach presented here is based o...

"... Multidimensional scaling (MDS) is the art of reconstructing pointsets (embeddings) from pairwise distance data, and as such it is at the basis of several approaches to nonlinear dimension reduction and manifold learning. At present, MDS lacks a unifying methodology as it consists of a discrete colle ..."

Multidimensional scaling (MDS) is the art of reconstructing pointsets (embeddings) from pairwise distance data, and as such it is at the basis of several approaches to nonlinear dimension reduction and manifold learning. At present, MDS lacks a unifying methodology as it consists of a discrete collection of proposals that differ in their optimization criteria, called “stress functions”. To correct this situation we propose (1) to embed many of the extant stress functions in a parametric family of stress functions, and (2) to replace the ad hoc choice among discrete proposals with a principled parameter selection method. This methodology yields the following benefits and problem solutions: (a) It provides guidance in tailoring stress functions to a given data situation, responding to the fact that no single stress function dominates all others across all data situations; (b) the methodology enriches the supply of available stress functions; (c) it helps our understanding of stress functions by replacing the comparison of discrete proposals with a characterization of the effect of parameters on embeddings; (d) it builds a bridge to graph drawing, which is the related but not identical art of constructing embeddings from graphs.

Abstract. To enable discovery in large, heterogenious information net-works a tool is needed that allows exploration in changing graph struc-tures and integrates advanced graph mining methods in an interactive visualization framework. We present the Creative Exploration Toolkit (CET), which consists of a state-of-the-art user interface for graph visu-alization designed towards explorative tasks and support tools for inte-gration and communication with external data sources and mining tools, especially the data-mining platform KNIME. All parts of the interface can be customized to fit the requirements of special tasks, including the use of node type dependent icons, highlighting of nodes and clus-ters. Through an evaluation we have shown the applicability of CET for structure-based analysis tasks. 1

... status, – a sidebar on the right which displays detailed information about a node, – and the workspace in the center, which is used for visualization. We currently use the Stress Minimization Layout =-=[15]-=- to determine the initial graph layout, followed by an overlap removal [8]. Nodes can be moved to create certain arrangements, selected for further action, and expanded by doubleclicking them. On expa...

Abstract. We present a tool for interactive exploration of graphs that integrates advanced graph mining methods in an interactive visualization framework. The tool enables efficient exploration and analysis of complex graph structures. For flexible integration of state-of-the-art graph mining methods, the viewer makes use of the open source data mining platform KNIME. In contrast to existing graph visualization interfaces, all parts of the interface can be dynamically changed to specific visualization re-quirements, including the use of node type dependent icons, methods for a marking if nodes or edges and highlighting and a fluent graph that allows for iterative growing, shrinking and abstraction of (sub)graphs. 1

... status, – a sidebar on the right which displays detailed information about a node, – and the workspace in the center, which is used for visualization. We currently use the Stress Minimization Layout =-=[3]-=- to determine the initial graph layout, which enables the user to interact with the graph: Nodes can be moved to create certain arrangements, nodes can be selected, and nodes can be expanded by double...

"... We show that rectilinear graph drawing, the core problem of bendminimum orthogonal graph drawing, and uniform edge-length drawing, the core problem of force-directed placement, are N P-hard even for embedded paths if subjected to orthogonal-ordering constraints. Submitted: ..."

We show that rectilinear graph drawing, the core problem of bendminimum orthogonal graph drawing, and uniform edge-length drawing, the core problem of force-directed placement, are N P-hard even for embedded paths if subjected to orthogonal-ordering constraints. Submitted:

... recently, other extensions of the stress term have been used for drawing graphs with explicitly formulated aesthetic criteria, such as the uniform scattering of the nodes in a graph over a unit disk =-=[20]-=-, penalizing node overlaps [15], or preserving a given topology [13]. JGAA, 15(1) 157–173 (2011) 159 (a) unconstrained (b) with radial constraints Figure 1: A social network (courtesy of Carola Lipp; ...

"... This paper presents LinkScope, a toolkit for interactive anal-ysis of text using node link graphs, with support for dynamic addition of attributes from tabular data. The interaction tech-nique draws on ideas from 3D modeling, mesh deformation, and static graph drawing to promote discovery of hidden ..."

This paper presents LinkScope, a toolkit for interactive anal-ysis of text using node link graphs, with support for dynamic addition of attributes from tabular data. The interaction tech-nique draws on ideas from 3D modeling, mesh deformation, and static graph drawing to promote discovery of hidden in-formation across a wide variety of graph types and analysis tasks. The key innovation of this work is the application of methods traditionally reserved for automated graph layout and clustering, to produce useful task-specific layout through dynamic interactions. Graph nodes are dynamically reposi-tioned using an interpolated decay function over a single node movement provided by a user. We describe several variants of the interpolation method, including coupling it with a fast local-cut algorithm for cluster selection. Compared to tradi-tional layout mechanisms the technique is particularly useful when meta-data nodes are added to a graph, increasing its connectivity. We show how the techniques can be used inter-actively to solve text analysis tasks including a case study on a collection of 16K awarded NSF grant proposals with meta-data and a corpus of New York Times news articles.

...so. Layouts The LinkScope analysis toolkit contains implementations of a number of force-directed graph layout algorithms including an optimized Fruchterman-Reingold layout [10], Binary stress layout =-=[14]-=-, FM3 layout [11] and the topic-based multidimensional scaling layout from [9]. The toolkit also uses layered layout based on Dk component-analysis [16] that attempts to lay out more connected compone...

"... In some applications of graph visualization, input edges have associated target lengths. Dealing with these lengths is a challenge, especially for large graphs. Stress models are often employed in this situation. However, the traditional full stress model is not scalable due to its reliance on an in ..."

In some applications of graph visualization, input edges have associated target lengths. Dealing with these lengths is a challenge, especially for large graphs. Stress models are often employed in this situation. However, the traditional full stress model is not scalable due to its reliance on an initial all-pairs shortest path calculation. A number of fast approximation algorithms have been proposed. While they work well for some graphs, the results are less satisfactory on graphs of intrinsically high dimension, because nodes overlap unnecessarily. We propose a solution, called the maxent-stress model, which applies the principle of maximum entropy to cope with the extra degrees of freedom. We describe a force-augmented stress majorization algorithm that solves the maxent-stress model. Numerical results 1 show that the algorithm scales well, and provides acceptable layouts for large, non-rigid graphs. This also has potential applications to scalable algorithms for statistical multidimensional scaling (MDS) with variable distances.

...f the parameter t, they did not give details on the implementation of the algorithm, so it is difficult to assess its scalability. Another related model is the binary stress model of Koren and Civril =-=[20]-=-. In that model, there is a distance of 0 between nodes sharing an edge, and a distance of 1 otherwise. The model is then ∑ ‖xi − x j‖ (i, j)∈E 2 ( + α ∑ ‖xi − x j‖ − 1 (i, j)/∈E ) 2 . Energy models o...